Consensus Coding Sequences of Human Breast and Colorectal Cancers

ABSTRACT

Analysis of 13,023 genes in 11 breast and 11 colorectal cancers revealed that individual tumors accumulate an average of ˜90 mutant genes but that only a subset of these contribute to the neoplastic process. Using stringent criteria to delineate this subset, we identified 189 genes (average of 11 per tumor) that were mutated at significant frequency. The vast majority of these genes were not known to be genetically altered in tumors and are predicted to affect a wide range of cellular functions, including transcription, adhesion, and invasion. These data define the genetic landscape of two human cancer types, provide new targets for diagnostic and therapeutic intervention and monitoring.

This invention was made using grant funds from the U.S. government.Under the term of the grants, the U.S. government retains certain rightsin the invention. Grants used include NIH grants CA 121113, CA 43460, CA57345, CA 62924, GM 07309, RR 017698, P30-CA43703, and CA109274, andDepartment of Defense grant DAMD17-03-1-0241.

TECHNICAL FIELD OF THE INVENTION

This invention is related to the area of cancer characterization. Inparticular, it relates to breast and colorectal cancers.

BACKGROUND OF THE INVENTION

It is widely accepted that human cancer is a genetic disease caused bysequential accumulation of mutations in oncogenes and tumor suppressorgenes (1). These tumor-specific (that is, somatic) mutations provideclues to the cellular processes underlying tumorigenesis and have provenuseful for diagnostic and therapeutic purposes. To date, however, only asmall fraction of the genes has been analyzed and the number and type ofalterations responsible for the development of common tumor types areunknown (2). In the past, the selection of genes chosen for mutationalanalyses in cancer has been guided by information from linkage studiesin cancer-prone families, identification of chromosomal abnormalities intumors, or known functional attributes of individual genes or genefamilies (2-4). The determination of the human genome sequence coupledwith improvements in sequencing and bioinformatic approaches have nowmade it possible, in principle, to examine the cancer cell genome in acomprehensive and unbiased manner. Such an approach not only providesthe means to discover other genes that contribute to tumorigenesis butcan also lead to mechanistic insights that are only evident through asystems biological perspective. Comprehensive genetic analyses of humancancers could lead to discovery of a set of genes, linked togetherthrough a shared phenotype, that point to the importance of specificcellular processes or pathways.

There is a continuing need in the art to identify genes and patterns ofgene mutations useful for identifying and stratifying individualpatients' cancers.

SUMMARY OF THE INVENTION

According to one embodiment of the invention a method is provided fordiagnosing breast cancer in a human. A somatic mutation in a gene or itsencoded cDNA or protein is determined in a test sample relative to anormal sample of the human. The gene is selected from the groupconsisting of those listed in FIG. 13 (Table S5). The sample isidentified as breast cancer when the somatic mutation is determined.

A method is provided for diagnosing colorectal cancer in a human. Asomatic mutation in a gene or its encoded cDNA or protein is determinedin a test sample relative to a normal sample of the human. The gene isselected from the group consisting of those listed in FIG. 14. (TableS6). The sample is identified as colorectal cancer if the somaticmutation is determined.

A method is provided for stratifying breast cancers for testingcandidate or known anti-cancer therapeutics. A CAN-gene mutationalsignature for a breast cancer is determined by determining at least onesomatic mutation in a test sample relative to a normal sample of ahuman. The at least one somatic mutation is in one or more genesselected from the group consisting of FIG. 13 (Table S5). A first groupof breast cancers that have the CAN-gene mutational signature is formed.Efficacy of a candidate or known anti-cancer therapeutic on the firstgroup is compared to efficacy on a second group of breast cancers thathas a different CAN-gene mutational signature. A CAN gene mutationalsignature which correlates with increased or decreased efficacy of thecandidate or known anti-cancer therapeutic relative to other groups isidentified.

A method is provided for stratifying colorectal cancers for testingcandidate or known anti-cancer therapeutics. A CAN-gene mutationalsignature for a colorectal cancer is determined by determining at leastone somatic mutation in a test sample relative to a normal sample of thehuman. The at least one somatic mutation is in one or more genesselected from the group consisting of FIG. 14. (Table S6). A first groupof colorectal cancers that have the CAN-gene mutational signature isformed. Efficacy of a candidate or known anti-cancer therapeutic on thefirst group is compared to efficacy on a second group of colorectalcancers that has a different CAN-gene mutational signature. A CAN genemutational signature is identified which correlates with increased ordecreased efficacy of the candidate or known anti-cancer therapeuticrelative to other groups.

A method is provided for characterizing a breast cancer in a human. Asomatic mutation in a gene or its encoded cDNA or protein is determinedin a test sample relative to a normal sample of the human. The gene isselected from the group consisting of those listed in FIG. 13 (TableS5).

Another method provided is for characterizing a colorectal cancer in ahuman. A somatic mutation in a gene or its encoded cDNA or protein isdetermined in a test sample relative to a normal sample of the human.The gene is selected from the group consisting of those listed in FIG.14 (Table S6).

These and other embodiments which will be apparent to those of skill inthe art upon reading the specification provide the art with

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A and 1B. Schematic of Mutation Discovery and Validation Screens.

FIG. 2. Mutation frequency of CAN-gene groups. CAN-genes were grouped byfunction using Gene Ontology groups, INTERPRO domains, and availableliterature. Bars indicate the fraction of tumors (35 breast or 35colorectal) with at least one mutated gene in the functional group.

FIG. 3. (FIG. S1) Codon mutation frequencies. Open bars, CCDS codons(n=7,479,318 in 13,023 genes); red bars, codons affected by basesubstitution mutations in breast cancers (n=789); blue bars, codonsaffected by base substitution mutations in colorectal cancers (n=669).

FIG. 4. (FIG. S2) CCDS genes excluded from analysis. One hundredthirty-four transcripts from 119 genes that closely matched more thanone genomic locus (large circle), and/or were located won the Ychromosome (small circle), were excluded from analysis.

FIG. 5. (Table 1.) Summary of somatic mutations

FIG. 6. (Table 2) Spectrum of single base substitutions

FIG. 7. (Table 3.) Functional classification of CAN-genes*

FIG. 8. (Table S1.) Primers used for PCR amplification and sequencing(page 1 of 1333 only; all primer sequences are publicly available in adownloadable file (1133427_som_tables.zip) at the website of the journalScience (www.sciencemag.org) under Supporting Online Material located atthe webpage /cgi/content/full/sci;1133427/DC1)

FIG. 9. (Table S2A.) Characteristics of the colorectal cancer samples.

FIG. 10. (Table S2B.) Characteristics of the breast cancer samples.

FIG. 11. (Table S3.) Distribution of mutations in individual cancers.

FIG. 12. (Table S4.) Somatic mutations identified in breast orcolorectal cancers.

FIG. 13. (Table S5.) Breast CAN-genes.

FIG. 14. (Table S6.) Colorectal CAN-genes.

DETAILED DESCRIPTION OF THE INVENTION

The inventors have developed methods for characterizing breast andcolorectal cancers on the basis of gene signatures. These signaturescomprise one or more genes which are mutated in a particular cancer. Thesignatures can be used as a means of diagnosis, prognosis,identification of metastasis, stratification for drug studies, and forassigning an appropriate treatment.

According to the present invention a mutation, typically a somaticmutation, can be determined by testing either a gene, its mRNA (orderived cDNA), or its encoded protein. Any method known in the art fordetermining a somatic mutation can be used. The method may involvesequence determination of all or part of a gene, cDNA, or protein. Themethod may involve mutation-specific reagents such as probes, primers,or antibodies. The method may be based on amplification, hybridization,antibody-antigen reactions, primer extension, etc. Any technique ormethod known in the art for determining a sequence-based feature may beused.

Samples for testing may be tissue samples from breast or colorectaltissue or body fluids or products that contain sloughed off cells orgenes or mRNA or proteins. Such fluids or products include breast milk,stool, breast discharge, intestinal fluid. Preferably the same type oftissue or fluid is used for the test sample and the normal sample. Thetest sample is, however, suspected of possible neoplastic abnormality,while the normal sample is not suspect.

Somatic mutations are determined by finding a difference between a testsample and a normal sample of a human. This criterion eliminates thepossibility of germline differences confounding the analysis. For breastcancer, the gene (or cDNA or protein) to be tested is any of those shownin FIG. 13 (Table S5). Particular genes which may be tested and usefulare gelsolin GSN, cadherin genes CDH10 and CDH20, actin and SMAD bindingprotein filamin B FLNB, and autocrine motility factor receptor AMFR.Additional useful genes include ATP-dependent transporter ATP8B1,intrinsic factor-cobalamin receptor CUBN, actin binding protein DBN1,and tectorin alpha TECTA. For colorectal cancer, the gene (or cDNA orprotein) to be tested is any of those shown in FIG. 14. (Table S6).Particular genes which may be tested and useful are ephrin receptorEPHB6, mixed lineage leukemia 3 gene (MLL3), and protein tyrosinephosphatase receptor PTPRD. Other genes which may be tested and usefulare polycystic kidney and hepatic disease 1 gene PKHD1, guanylatecyclase 1 GUCY1A2, transcription factor TBX22, exocyst complex componentSEC8L1, and tubulin tyrosine ligase TTLL3. Any somatic mutation may beinformative. Particular mutations which may be used are shown in FIG. 12(Table S4).

The number of genes or mutations that may be useful in forming asignature of a breast or colorectal cancer may vary from one totwenty-five. At least two, three, four, five, six, seven or more genesmay be used. The mutations are typically somatic mutations andnon-synonymous mutations. Those mutations described here are withincoding regions. Other non-coding region mutations may also be found andmay be informative.

In order to test candidate or already-identified therapeutic agents todetermine which patients and tumors will be sensitive to the agents,stratification on the basis of signatures can be used. One or moregroups with a similar mutation signature will be formed and the effectof the therapeutic agent on the group will be compared to the effect ofpatients whose tumors do not share the signature of the group formed.The group of patients who do not share the signature may share adifferent signature or they may be a mixed population of tumor-bearingpatients whose tumors bear a variety of signatures.

Efficacy can be determined by any of the standard means known in theart. Any index of efficacy can be used. The index may be life span,disease free remission period, tumor shrinkage, tumor growth arrest,improvement of quality of life, decreased side effects, decreased pain,etc. Any useful measure of patient health and well-being can be used. Inaddition, in vitro testing may be done on tumor cells that haveparticular signatures. Tumor cells with particular signatures can alsobe tested in animal models.

Once a signature has been correlated with sensitivity or resistance to aparticular therapeutic regimen, that signature can be used forprescribing a treatment to a patient. Thus determining a signature isuseful for making therapeutic decisions. The signature can also becombined with other physical or biochemical findings regarding thepatient to arrive at a therapeutic decision. A signature need not be thesole basis for making a therapeutic decision.

An anti-cancer agent associated with a signature may be, for example,docetaxel, paclitaxel, topotecan, adriamycin, etoposide, fluorouracil(5-FU), or cyclophosphamide. The agent may be an alkylating agent (e.g.,nitrogen mustards), antimetabolites (e.g., pyrimidine analogs),radioactive isotopes (e.g., phosphorous and iodine), miscellaneousagents (e.g., substituted ureas) and natural products (e.g., vincaalkyloids and antibiotics). The therapeutic agent may be allopurinolsodium, dolasetron mesylate, pamidronate disodium, etidronate,fluconazole, epoetin alfa, levamisole HCL, amifostine, granisetron HCL,leucovorin calcium, sargramostim, dronabinol, mesna, filgrastim,pilocarpine HCL, octreotide acetate, dexrazoxane, ondansetron HCL,ondansetron, busulfan, carboplatin, cisplatin, thiotepa, melphalan HCL,melphalan, cyclophosphamide, ifosfamide, chlorambucil, mechlorethamineHCL, carmustine, lomustine, polifeprosan 20 with carmustine implant,streptozocin, doxorubicin HCL, bleomycin sulfate, daunirubicin HCL,dactinomycin, daunorucbicin citrate, idarubicin HCL, plimycin,mitomycin, pentostatin, mitoxantrone, valrubicin, cytarabine,fludarabine phosphate, floxuridine, cladribine, methotrexate,mercaptipurine, thioguanine, capecitabine, methyltestosterone,nilutamide, testolactone, bicalutamide, flutamide, anastrozole,toremifene citrate, estramustine phosphate sodium, ethinyl estradiol,estradiol, esterified estrogens, conjugated estrogens, leuprolideacetate, goserelin acetate, medroxyprogesterone acetate, megestrolacetate, levamisole HCL, aldesleukin, irinotecan HCL, dacarbazine,asparaginase, etoposide phosphate, gemcitabine HCL, altretamine,topotecan HCL, hydroxyurea, interferon alpha-2b, mitotane, procarbazineHCL, vinorelbine tartrate, E. coli L-asparaginase, ErwiniaL-asparaginase, vincristine sulfate, denileukin diftitox, aldesleukin,rituximab, interferon alpha-2a, paclitaxel, docetaxel, BCG live(intravesical), vinblastine sulfate, etoposide, tretinoin, teniposide,porfimer sodium, fluorouracil, betamethasone sodium phosphate andbetamethasone acetate, letrozole, etoposide citrororum factor, folinicacid, calcium leucouorin, 5-fluorouricil, adriamycin, cytoxan, ordiamino-dichloro-platinum.

The signatures of CAN genes according to the present invention can beused to determine an appropriate therapy for an individual. For example,a sample of a tumor (e.g., a tissue obtained by a biopsy procedure, suchas a needle biopsy) can be provided from the individual, such as beforea primary therapy is administered. The gene expression profile of thetumor can be determined, such as by a nucleic acid array (or proteinarray) technology, and the expression profile can be compared to adatabase correlating signatures with treatment outcomes. Otherinformation relating to the human (e.g., age, gender, family history,etc.) can factor into a treatment recommendation. A healthcare providercan make a decision to administer or prescribe a particular drug basedon the comparison of the CAN gene signature of the tumor and informationin the database. Exemplary healthcare providers include doctors, nurses,and nurse practitioners. Diagnostic laboratories can also provide arecommended therapy based on signatures and other information about thepatient.

Following treatment with a primary cancer therapy, the patient can bemonitored for an improvement or worsening of the cancer. A tumor tissuesample (such as a biopsy) can be taken at any stage of treatment. Inparticular, a tumor tissue sample can be taken upon tumor progression,which can be determined by tumor growth or metastasis. A CAN genesignature can be determined, and one or more secondary therapeuticagents can be administered to increase, or restore, the sensitivity ofthe tumor to the primary therapy.

Treatment predictions may be based on pre-treatment gene signatures.Secondary or subsequent therapeutics can be selected based on thesubsequent assessments of the patient and the later signatures of thetumor. The patient will typically be monitored for the effect on tumorprogression.

A medical intervention can be selected based on the identity of the CANgene signature. For example, individuals can be sorted intosubpopulations according to their genotype. Genotype-specific drugtherapies can then be prescribed. Medical interventions includeinterventions that are widely practiced, as well as less conventionalinterventions. Thus, medical interventions include, but are not limitedto, surgical procedures, administration of particular drugs or dosagesof particular drugs (e.g., small molecules, bioengineered proteins, andgene-based drugs such as antisense oligonucleotides, ribozymes, genereplacements, and DNA- or RNA-based vaccines), including FDA-approveddrugs, FDA-approved drugs used for off-label purposes, and experimentalagents. Other medical interventions include nutritional therapy,holistic regimens, acupuncture, meditation, electrical or magneticstimulation, osteopathic remedies, chiropractic treatments, naturopathictreatments, and exercise.

Four important points have emerged from our comprehensive mutationalanalysis of human cancer. First, a relatively large number of previouslyuncharacterized CAN-genes exist in breast and colorectal cancers andthese genes can be discovered by unbiased approaches such as that usedin our study. These results support the notion that large-scalemutational analyses of other tumor types will prove useful foridentifying genes not previously known to be linked to human cancer.

Second, our results suggest that the number of mutational eventsoccurring during the evolution of human tumors from a benign to ametastatic state is much larger than previously thought. We found thatbreast and colorectal cancers harbor an average of 52 and 67non-synonymous somatic mutations in CCDS genes, of which an average of 9and 12, respectively, were in CAN-genes. FIG. 11(Table S3). These datacan be used to estimate the total number of nonsynonymous mutations incoding genes that arise in a “typical” cancer through sequential roundsof mutation and selection. Assuming that the mutation prevalence ingenes that have not yet been sequenced is similar to that of the genesso far analyzed, we estimate that there are 81 and 105 mutant genes(average, 93) in the typical colorectal or breast cancer, respectively.Of these, an average of 14 and 20, respectively, would be expected to beCAN-genes. In addition to the CAN-genes, there were other mutated CCDSgenes that were likely to have been selected for during tumorigenesisbut were not altered at a frequency high enough to warrant confidence intheir interpretation.

A third point emerging from our study is that breast and colorectalcancers show substantial differences in their mutation spectra. Incolorectal cancers, a bias toward C:G to T:A transitions at 5′-CpG-3′sites has been previously noted in TP53 (42). Our results suggest thatthis bias is genome-wide rather than representing a selection forcertain nucleotides within TP53. This bias may reflect a more extensivemethylation of 5′-CpG-3′ dinucleotides in colorectal cancers than inbreast cancers or the effect of dietary carcinogens (43, 44). In breastcancers, the fraction of mutations at 5′-TpC-3′ sites was far higher inthe CCDS genes examined in this study than previously reported for TP53(37). It has been noted that a small fraction of breast tumors may havea defective repair system, resulting in 5′-TpC-3′ mutations (15). Ourstudies confirm that some breast cancers have higher fractions of5′-TpC-3′ mutations than others, but also show that mutations at thisdinucleotide are generally more frequent than in colorectal cancers(FIGS. 6 and 11; Tables 2 and S3).

Finally, our results reveal that there are substantial differences inthe panel of CAN-genes mutated in the two tumor types (FIG. 7; Table 3).For example, metalloproteinase genes were mutated in a large fraction ofcolorectal but only in a small fraction of breast cancers (FIGS. 13 and14; Tables S5 and S6). Transcriptional regulator genes were mutated in ahigh fraction of both breast and colorectal tumors, but the specificgenes affected varied according to tumor type (FIG. 7; Table 3). Therewas also considerable heterogeneity among the CAN-genes mutated indifferent tumor specimens derived from the same tissue type (FIGS.12-14; Tables S4, S5, and S6). It has been documented that virtually allbiochemical, biological, and clinical attributes are heterogeneouswithin human cancers of the same histologic subtype (45). Our datasuggest that differences in the CAN-genes mutated in various tumorscould account for a major part of this heterogeneity. This might explainwhy it has been so difficult to correlate the behavior, prognosis, orresponse to therapy of common solid tumors with the presence or absenceof a single gene alteration; such alterations reflect only a smallcomponent of each tumor's mutational composition. On the other hand,disparate genes contributing to cancer are often functionallyequivalent, affecting net cell growth through the same molecular pathway(1). Thus, TP53 and MDM2 mutations exert comparable effects on cells, asdo mutations in RB1, CDKN2A (p16), CCND1 and CDK4. It will be ofinterest to determine whether a limited number of pathways include mostCAN-genes, a possibility consistent with the groupings in FIG. 2 andFIG. 7 (Table 3).

Like a draft version of any genome project, our study has limitations.First, only genes present in the current version of CCDS were analyzed.There are ˜5000 genes for which excellent supporting evidence exists butare not yet included in the CCDS database (46). Second, we were not ableto successfully sequence ˜10% of the bases within the coding sequencesof the 13,023 CCDS genes (equivalent to 1,302 unsequenced genes). Third,although our screen would be expected to identify the most common typesof mutations found in cancers, some genetic alterations, includingmutations in non-coding genes, mutations in non-coding regions of codinggenes, relatively large deletions or insertions, amplifications, andtranslocations, would not be detectable by the methods we used. Futurestudies employing a combination of different technologies, such as thoseenvisioned by The Cancer Genome Atlas Project (TCGA) (47), will be ableto address these issues.

The results of this study inform future cancer genome sequencing effortsin several important ways.

(i) A major technical challenge of such studies will be discerningsomatic mutations from the large number of sequence alterationsidentified. In our study, 557,029 non-synonymous sequence alterationswere detected in the Discovery Screen but after subsequent analyses only0.23% of these were identified as legitimate somatic mutations (FIG. 1).Less than 10% of nonsynonymous alterations were known polymorphisms;many of the rest were uncommon germline variants or sequence artifactsthat were not reproducible. Inclusion of matched normal samples andsequencing both strands of each PCR product would reduce false positivesin the Discovery Screen but would increase the cost of sequencing byfour-fold. Although recently developed sequencing methods could reducethe cost of such studies in the future (48), the higher error rates ofthese approaches may result in an even lower ratio of bona fide somaticmutations to putative alterations.

(ii) Another technical issue is that careful design of primers isimportant to eliminate sequence artifacts due to the inadvertentamplification and sequencing of related genes. The primer pairs thatresulted in successful amplification and sequencing represent a valuableresource in this regard. Even with well-designed primers, it isessential to examine any observed mutation to ensure that it is notfound as a normal variant in a related gene.

(iii) Although it is likely that studies of other solid tumor types willalso identify a large number of somatic mutations, it will be importantto apply rigorous approaches to identify those mutations that have beenselected for during tumorigenesis. Statistical techniques, such as thoseused in this study or described by Greenman et al. (11), can providestrong evidence for selection of mutated genes. These approaches arelikely to improve as more cancer genomic sequencing data is accumulatedthrough The Cancer Genome Atlas Project (47) and other projects nowunderway.

(iv) There has been much discussion about which genes should be thefocus of future sequencing efforts. Our results suggest that many genesnot previously implicated in cancer are mutated at significant levelsand may provide novel clues to pathogenesis. From these data, it wouldseem that large-scale unbiased screens of coding genes may be moreinformative than screens based on previously defined criteria.

1491 (v) The results also raise questions about the optimum number oftumors of any given type that should be assessed in a cancer genomestudy. Our study was designed to determine the nature and types ofalterations present in an “average” breast or colorectal cancer and todiscover genes mutated at reasonably high frequencies. Our power todetect genes mutated in more than 20% of tumors of a given type was 90%,but only 50% of genes mutated in 6% of tumors would have beendiscovered. To detect genes mutated in 6% or 1% of tumors with >99%probability in a Discovery Screen would require sequence determinationof at least 75 or 459 tumors, respectively. Though it will be impossibleto detect all mutations that may occur in tumors, strategies that wouldidentify the most important ones at an affordable cost can be envisionedon the basis of the data and analysis reported herein.

(vi) Ultimately, the sequences of entire cancer genomes, includingintergenic regions, will be obtainable. Our studies demonstrate theinherent difficulties in determining the significance of somaticmutations, even those that alter the amino acid sequence ofhighly-annotated and well-studied genes. Establishing the significanceof mutations in non-coding regions of the genome will likely be muchmore difficult. Until new tools for solving this problem becomeavailable, it is likely that gene-centric analyses of cancer will bemore useful.

Our results provide a large number of future research opportunities inhuman cancer. For genetics, it will be of interest to elucidate thetiming and extent of CAN-gene mutations in breast and colorectalcancers, whether these genes are mutated in other tumor types, andwhether germline variants in CAN-genes are associated with cancerpredisposition. For immunology, the finding that tumors contain anaverage of ˜90 different amino acid substitutions not present in anynormal cell can provide novel approaches to engender anti-tumorimmunity. For epidemiology, the remarkable difference in mutationspectra of breast and colorectal cancers suggests the existence oforgan-specific carcinogens. For cancer biology, it is clear that nocurrent animal or in vitro model of cancer recapitulates the geneticlandscape of an actual human tumor. Understanding and capturing thislandscape and its heterogeneity may provide models that moresuccessfully mimic the human disease. For epigenetics, it is possiblethat a subset of CAN-genes can also be dysregulated in tumors throughchanges in chromatin or DNA methylation rather than through mutation.For diagnostics, the CAN-genes define a relatively small subset of genesthat could prove useful as markers for neoplasia. Finally, some of thesegenes, particularly those on the cell surface or those with enzymaticactivity, may prove to be good targets for therapeutic development.

The above disclosure generally describes the present invention. Allreferences disclosed herein are expressly incorporated by reference. Amore complete understanding can be obtained by reference to thefollowing specific examples which are provided herein for purposes ofillustration only, and are not intended to limit the scope of theinvention.

EXAMPLES

To begin the systematic study of the cancer genome, we have examined amajor fraction of human genes in two common tumor types, breast andcolorectal cancers. These cancers were chosen for study because of theirsubstantial clinical significance world-wide: together, they account for˜2.2 million cancer diagnoses (20% of the total) and ˜940,000 cancerdeaths each year (14% of the total) (5). For genetic evaluation of thesetumors, we focused on a set of protein coding genes, termed theconsensus coding sequences (CCDS) that represent the most highly curatedgene set currently available (6). The CCDS database contains full-lengthprotein coding genes that have been defined by extensive manual curationand computational processing and have gene annotations that areidentical among reference databases.

The goals of this study were three-fold: (i) to develop a methodologicalstrategy for conducting genome-wide analyses of cancer genes in humantumors; (ii) to determine the spectrum and extent of somatic mutationsin human tumors of similar and different histologic types; and (iii) toidentify new cancer genes and molecular pathways that could lead toimprovements in diagnosis or therapy.

Example 1—Cancer Mutation Discovery Screen

The initial step toward achieving these goals was the development ofmethods for high-throughput identification of somatic mutations incancers. These methods included those for primer design, polymerasechain reaction (PCR), sequencing, and mutational analysis (FIG. 1). Thefirst component involved extraction of all protein coding sequences fromthe CCDS genes. A total of 120,839 non-redundant exons and adjacentintronic sequences were obtained from 14,661 different transcripts inCCDS. These sequences were used to design primers for PCR amplificationand sequencing of exons and adjacent splice sites. Primers were designedusing a number of criteria to ensure robust amplification and sequencingof template regions (7). While most exons could be amplified in a singlePCR reaction, we found that exons larger than 350 bp were moreeffectively amplified as multiple overlapping amplicons. One member ofevery pair of PCR primers was tailed with a universal primer sequencefor subsequent sequencing reactions. A total of 135,483 primer pairsencompassing ˜21 Mb of genomic sequence were designed in this manner(FIG. 8; Table S1).

Eleven cell lines or xenografts of each tumor type (breast andcolorectal carcinomas) were used in the Discovery Screen (FIGS. 9-10;Tables S2A and S2B). Two matching normal samples were used as controlsto help identify normal sequence variations and amplicon-specificsequencing artifacts such as those associated with GC-rich regions. Atotal of ˜3 million PCR products were generated and directly sequenced,resulting in 465 Mb of tumor sequence.

Sequence data were assembled for each amplicon and evaluated for qualitywithin the target region using software specifically designed for thispurpose (7). The target region of each exon included all coding bases aswell as the four intronic bases at both the 5′ and 3′ ends that serve asthe major splice recognition sites. In order for an amplicon to beconsidered successfully analyzed, we required that ≧90% of bases in thetarget region have a Phred quality score (defined as −10 [log₁₀(rawper-base error)]) of at least 20 in at least three quarters of the tumorsamples analyzed (8). This quality cutoff was chosen to provide highsensitivity for mutation detection while minimizing false positives.Using these criteria, 93% of the 135,483 amplicons and 91% of the totaltargeted bases in CCDS were successfully analyzed for potentialalterations.

Examination of sequence traces from these amplicons revealed a total of816,986 putative nucleotide changes. As the vast majority of changesthat did not affect the amino acid sequence (i.e., synonymous or silentsubstitutions) were likely to be non-functional, these changes were notanalyzed further. The remaining 557,029 changes could represent germlinevariants, artifacts of PCR or sequencing, or bona fide somaticmutations. Several bioinformatic and experimental steps were employed todistinguish among these possibilities. First, any alterations that werealso present in either of the two normal samples included in theDiscovery Screen were removed, as these were likely to represent commongermline polymorphisms or sequence artifacts. Second, as these twonormal control samples would be expected to contain only a subset ofknown variants, any change corresponding to a validated germlinepolymorphism found in single nucleotide polymorphism (SNP) databases wasalso removed (7). Finally, the sequence trace of each potentialalteration was visually inspected in order to remove false positivecalls in the automated analysis. The combination of these data analysisefforts was efficient, removing ˜96% of the potential alterations andleaving 29,281 for further scrutiny (FIG. 1).

To ensure that the observed mutations did not arise artifactually duringthe PCR or sequencing steps, the regions containing them wereindependently re-amplified and re-sequenced in the corresponding tumors.This step removed 9,295 alterations. The regions containing the putativemutations were then sequenced in matched normal DNA samples to determinewhether the mutations were truly somatic: 18,414 changes were observedto be present in the germline of these patients, representing variantsnot currently annotated in SNP databases, and were excluded. As a finalstep, the remaining 1,572 putative somatic mutations were carefullyexamined in silico to ensure that the alterations did not arise frommistargeted sequencing of highly related regions occurring elsewhere inthe genome (7). Alterations in such duplicated regions may appear to besomatic when there is loss of one or both alleles of the target regionin the tumor and when the selected primers closely match and thereforeamplify similar areas of the genome. A total of 265 changes in closelyrelated regions were excluded in this fashion, resulting in a total of1,307 confirmed somatic mutations in 1,149 genes (FIG. 5; Table 1).

Example 2—Validation Screen

To evaluate the prevalence and spectrum of somatic mutations in these1,149 genes, we determined their sequence in additional tumors of thesame histologic type (FIGS. 1, 9, 10; Tables S2A and S2B). Genes mutatedin at least one breast or colorectal tumor in the Discovery Screen wereanalyzed in 24 additional breast or colorectal tumors, respectively.This effort involved 453,024 additional PCR and sequencing reactions,encompassing 77 Mb of tumor DNA. A total of 133,693 putative changeswere identified in the Validation Screen. Methods similar to thoseemployed in the Discovery Screen were used to exclude silent changes,known and novel germline variants, false positives arising from PCR orsequencing artifacts, and apparent changes that were likely due toco-amplification of highly related genes. Additionally, any changescorresponding to germline variants not found in SNP databases butidentified in the Discovery Screen were excluded. The regions containingthe remaining 4,948 changes were re-amplified and re-sequenced in thecorresponding tumors (to ensure reproducibility) and in matched normaltissue to determine if they were somatic. An additional 365 somaticmutations in 236 genes were identified in this manner. In total, 921 and751 somatic mutations were identified in breast and colorectal cancers,respectively (FIGS. 1, 5, and 12; Tables 1 and S4).

Example 3—Mutation Spectrum

The great majority of the 1,672 mutations observed in the Discovery orValidation Screens were single base substitutions: 81% of the mutationswere missense, 7% were nonsense, and 4% altered splice sites (FIG. 5;Table 1). The remaining 8% were insertions, deletions, and duplicationsranging from one to 110 nucleotides in length. Though the fraction ofmutations that were single base substitutions was similar in breast andcolorectal cancers, the spectrum and nucleotide contexts of thesubstitution mutations were very different between the two tumor types.The most striking of these differences occurred at C:G base pairs: 59%of the 696 colorectal cancer mutations were C:G to T:A transitions whileonly 7% were C:G to G:C transversions (FIGS. 6 and 11; Tables 2 and S3).In contrast, only 35% of the mutations in breast cancers were C:G to T:Atransitions, while 29% were C:G to G:C transversions. In addition, alarge fraction (44%) of the mutations in colorectal cancers were at5′-CpG-3′ dinucleotide sites but only 17% of the mutations in breastcancers occurred at such sites. This 5′-CpG-3′ preference led to anexcess of nonsynonymous mutations resulting in changes of arginineresidues in colorectal cancers though not in breast cancers (FIG. S1).In contrast, 31% of mutations in breast cancers occurred at 5′-TpC-3′sites (or complementary 5′-GpA-3′ sites), while only 11% of mutations incolorectal cancers occurred at these dinucleotide sites. The differencesnoted above were all highly significant (P<0.0001) (7) and havesubstantial implications for the mechanisms underlying mutagenesis inthe two tumor types.

Example 4—Distinction Between Passenger and Non-Passenger Mutations

Somatic mutations in human tumors can arise either through selection offunctionally important alterations via their effect on net cell growthor through accumulation of non-functional “passenger” alterations thatarise during repeated rounds of cell division in the tumor or in itsprogenitor stem cell. In light of the relatively low rates of mutationin human cancer cells (9, 10), distinction between selected andpassenger mutations is generally not required when the number of genesand tumors analyzed is small. In large-scale studies, however, suchdistinctions are of paramount importance (11, 12). For example, it hasbeen estimated that nonsynonymous passenger mutations are present at afrequency no higher than ˜1.2 per Mb of DNA in cancers of the breast orcolon (13-15). As we assessed 542 Mb of tumor DNA, we would thereforehave expected to observe ˜650 passenger mutations. We actually observed1,672 mutations (FIG. 5; Table 1), many more than what would have beenpredicted to occur by chance (P<1×10⁻¹⁰) (7). Moreover, the frequency ofmutations in the Validation Screen was significantly higher than in theDiscovery Screen (5.8 versus 3.1 mutations per Mb, P<1×10⁻¹°, FIG. 5;Table 1). The mutations in the Validation Screen were also enriched fornonsense, insertion, deletion, duplication, and splice site changescompared to the Discovery Screen; each of these would be expected tohave a functional effect on the encoded proteins.

To distinguish genes likely to contribute to tumorigenesis from those inwhich passenger mutations occurred by chance, we first excluded genesthat were not mutated in the Validation Screen. We next developedstatistical methods to estimate the probability that the number ofmutations in a given gene was greater than expected from the backgroundmutation rate. For each gene, this analysis incorporated the number ofsomatic alterations observed in either the Discovery or ValidationScreen, the number of tumors studied, and the number of nucleotides thatwere successfully analyzed (as indicated by the number of bases withPhred quality scores ≧20). Because the mutation frequencies varied withnucleotide type and context and were different in breast versuscolorectal cancers (FIG. 6; Table 2), these factors were included in thecalculations. The output of this analysis was a cancer mutationprevalence (CaMP) score for each gene analyzed. The CaMP score reflectsthe probability that the number of mutations actually observed in a geneis higher than that expected to be observed by chance given thebackground mutation rate; its derivation is based on principlesdescribed in the Supporting Online Material. The use of the CaMP scorefor analysis of somatic mutations is analogous to the use of the LODscore for linkage analysis in familial genetic settings. For example,90% of the genes with CaMP scores >1.0 are predicted to have mutationfrequencies higher than the background mutation frequency.

Example 5—Candidate Cancer Genes

A complete list of the somatic mutations identified in this study isprovided in FIG. 12; Table S4. Validated genes with CaMP scores greaterthan 1.0 were considered to be candidate cancer genes (CAN-genes). Thecombination of experimental validation and statistical calculationthereby yielded four nested sets of genes: of 13,023 genes evaluated,1,149 were mutated, 242 were validated, and 191 were CAN-genes. Amongthese, the CAN-genes were most likely to have been subjected tomutational selection during tumorigenesis. There were 122 and 69CAN-genes identified in breast and colorectal cancers, respectively(FIGS. 13 and 14; Tables S5 and S6). Individual breast cancers examinedin the Discovery Screen harbored an average of 12 (range 4 to 23) mutantCAN-genes while the average number of CAN-genes in colorectal cancerswas 9 (range 3 to 18) (FIG. 11; Table S3). Interestingly, each cancerspecimen of a given tumor type carried its own distinct CAN-genemutational signature, as no cancer had more than six mutant CAN-genes incommon with any other cancer (FIGS. 12-14; Tables S4, S5, and S6).

CAN-genes could be divided into three classes: (a) genes previouslyobserved to be mutationally altered in human cancers; (b) genes in whichno previous mutations in human cancers had been discovered but had beenlinked to cancer through functional studies; and (c) genes with noprevious strong connections to neoplasia.

(a) The re-identification of genes that had been previously shown to besomatically mutated in cancers represented a critical validation of theapproach used in this study. All of the CCDS genes previously shown tobe mutated in >10% of either breast or colorectal cancers were found tobe CAN-genes in the current study. These included TP53 (2), APC (2),KRAS (2), SMAD4 (2), and FBXW7 (CDC4) (16) (FIGS. 12-14; Tables S4, S5and S6). In addition, we identified mutations in genes whose mutationprevalence in sporadic cancers was rather low. These genes includedEPHA3 (17), MRE11A (18), NF1 (2), SMAD2 (19, 20), SMAD3 (21), TCF7L2(TCF4) (22), BRCA1 (2) and TGFBRH (23). We also detected mutations ingenes that had been previously found to be altered in human tumors butnot in the same tumor type identified in this study. These includedguanine nucleotide binding protein, alpha stimulating GNAS (24),kelch-like ECH-associated protein KEAP1 (25), RET proto-oncogene (2),and transcription factor TCF1 (26). Finally, we found mutations in anumber of genes that have been previously identified as targets oftranslocation or amplification in human cancers. These includednucleoporin NUP214 (2), kinesin receptor KTN1 (27), DEAD box polypeptide10 DDX10 (28), glioma-associated oncogene homolog 1 GLI1 (29), and thetranslocation target gene of the runt related transcription factor 1RUNX1T1 (MTG8) (2). We conclude that if these genes had not already beendemonstrated to play a causative role in human tumors, they would havebeen discovered through the approach taken in this study. By analogy,the 176 other CAN-genes in FIGS. 13 and 14 (Tables S5 and S6) are likelyto play important roles in breast, colorectal, and perhaps other typesof cancers.

(b) Although genetic alterations currently provide the most reliableindicator of a gene's importance in human neoplasia (1, 30), there aremany other genes which are thought to play key roles on the basis offunctional or expression studies. Our study provides genetic evidencesupporting the importance of several of these genes in neoplasia. Forexample, we discovered intragenic mutations in the ephrin receptor EPHB6(31), mixed-lineage leukemia 3 gene (MLL3) (32), gelsolin GSN (33),cadherin genes CDH10 and CDH20, actin and SMAD binding protein filamin BFLNB (34), protein tyrosine phosphatase receptor PTPRD (35), andautocrine motility factor receptor AMFR (36).

(c) In addition to the genes noted above, our study revealed a largenumber of genes that had not been strongly suspected to be involved incancer. These included polycystic kidney and hepatic disease 1 genePKHD1, guanylate cyclase 1 GUCY1A2, transcription factor TBX22, exocystcomplex component SEC8L1, tubulin tyrosine ligase TTLL3, ATP-dependenttransporter ATP8B1, intrinsic factor-cobalamin receptor CUBN, actinbinding protein DBN1, and tectorin alpha TECTA. In addition, sevenCAN-genes corresponded to genes for which no biologic role has yet beenestablished.

We examined the distribution of mutations within CAN-gene products tosee if clustering occurred in specific regions or functional domains. Inaddition to the well documented hotspots in TP53 (37) and KRAS (38), weidentified three mutations in GNAS in colorectal cancers that affected asingle amino acid residue (R201). Alterations of this residue havepreviously been shown to lead to constitutive activation of the encodedG protein α_(s) through inhibition of GTPase activity (24). Twomutations in the EGF-like gene EGFL6 in breast tumors affected the samenucleotide position and resulted in a L508F change in the MAM adhesiondomain. A total of seven genes had alterations located within five aminoacid residues of each other, and an additional 12 genes had clusteringof multiple mutations within a specific protein domain (13 to 78 aminoacids apart). Thirty-one of 40 of these changes affected residues thatwere evolutionarily conserved. Although the effects of these alterationsare unknown, their clustering suggests specific roles for the mutatedregions in the neoplastic process.

Example 6—CAN-Gene Groups

An unbiased screen of a large set of genes can provide insights intopathogenesis that would not be apparent through single gene mutationalanalysis. This has been exemplified by large scale mutagenesis screensin experimental organisms (39-41). We therefore attempted to assign eachCAN-gene to a functional group based on Gene Ontology (GO) MolecularFunction or Biochemical process groups, the presence of specificINTERPRO sequence domains, or previously published literature (FIG. 7;Table 3) and (FIG. 2). Several of the groups identified in this way wereof special interest. For example, 22 of the 122 (18%) breast CAN-genesand 13 of the 69 (19%) colorectal CAN-genes were transcriptionalregulators. At least one of these genes was mutated in more than 80% ofthe tumors of each type. Zinc-finger transcription factors wereparticularly highly represented (8 genes mutated collectively in 43% ofbreast cancer samples). Similarly, genes involved in cell adhesionrepresented ˜22% of CAN-genes and affected more than two thirds oftumors of either type. Genes involved in signal transduction represented˜23% of CAN-genes and at least one such gene was mutated in 77% and 94%of the breast and colorectal cancer samples, respectively. Subsets ofthese groups were also of interest and included metalloproteinases (partof the cell adhesion and motility group and mutated in 37% of colorectalcancers), and G proteins and their regulators (part of the signaltransduction group and altered in 43% of breast cancers). These datasuggest that dysregulation of specific cellular processes aregenetically selected during neoplasia and that distinct members of eachgroup may serve similar roles in different tumors.

Example 7—Materials and Methods

Gene Selection.

The Consensus Coding DNA Sequence database (CCOS) represents a highlycurated collection of 14,795 transcripts from 13,142 genes(www.ncbi.nlm.nih.gov/CCOSI). For inclusion in CCOS, genomic coordinatesdefining the transcript coding sequence must be identical in Ensembl andRefSeq databases. The transcripts must have canonical start and stopcodons and consensus splice sites, not have in-frame stop codons, and betranslatable from the reference genome sequence without frameshifts.Finally, CCOS transcripts must be supported by transcript and proteinhomology and inter-species conservation. We examined all CCOStranscripts and excluded those that were located at multiple locationsin the genome through gene duplication (113 transcripts) or were presenton the Y chromosome (21 additional transcripts) (FIG. S1). The remaining14,661 CCOS transcripts from 13,023 genes were selected for mutationalanalysis.

Bioinformatic Resources.

CCOS gene and transcript coordinates (release 1, Mar. 2, 2005), humangenome sequences, and single nucleotide polymorphisms were obtained fromthe UCSC Santa Cruz Genome Bioinformatics Site (http://genome.ucsc.edu).Homology searches in the human and mouse genomes were performed usingthe BLAST-like alignment tool BLAT (S1) and In Silico PCR(http://qenome.ucsc.edu/cqi-bin/hqPcr). All genomic positions correspondto UCSC Santa Cruz hg17 build 35.1 human genome sequence. The −3.4 MSNPs of dbSNP (release 125) that have been validated through the HapMapproject (S2) were used for automated removal of known polymorphisms.

Primer Design.

For each transcript, genomic sequences comprising the entire codingregion of each exon as well as flanking intronic sequences and 5′ UTRand 3′ UTR sequences were extracted. Primer pairs for PCR amplificationand sequencing of each coding exon were generated using Primer3(http://frodo.wi.mit.edu/cqi-bin/primer3/primer3 www.cqi) (S3). Forwardand reverse PCR primers were required to be located no closer than 50 bpto the target exon boundaries, and genomic positions with knownpolymorph isms were avoided in the five 3′-most bases of the primers.Exons larger than 350 bp were analyzed as multiple overlappingamplicons. PCR products were designed to range in size from 300 to 600bp, which was considered optimal for amplification, purification, andsequencing. To minimize amplification of homologous genomic sequences,primer pairs were filtered using UCSC In Silico PCR and only pairsyielding a single product were used. 0.33 Mb (−1.5%) of target genomicsequence was excluded from further analysis due to a lack of suitableamplification and sequencing primers. A total of 135,483 primer pairsencompassing −21 Mb of target sequence were successfully designed. Auniversal sequencing primer (M13 forward, 5′-GTAAAACGACGGCCAGT-3; SEQ IDNO: 1) was appended to the 5′ end of the primer in the pair with thesmallest number of mono- and dinucleotide repeats between itself and thetarget exon. Primer sequences are listed in FIG. 8; Table S1.

Tumor Samples.

DNA samples from ductal breast carcinoma cell lines and matched normalmammary tissue or peripheral blood lines were obtained from AmericanType Culture Collection (Manassas, Va.) or from A. Gazdar (S4, S5).Primary breast tumor and surrounding normal surgical tissue specimensisolated from node positive patients at Palmetto Health Richland orBaptist Hospitals were obtained through the South Carolina Cancer CenterTissue Bank. Each tissue sample was flash frozen within 30 minutes ofexcision, and stored at −80° C. Surgically removed colorectal tumorswere disaggregated and implanted into nude mice or into in vitro cultureconditions as described previously (S6, S7). DNA was prepared within 3passages after xenograft establishment. Characteristics of the tumorsamples used in this study are listed in FIGS. 9-10; Tables S2A and S2B.No tumor used in this study was mismatch repair deficient as assessedwith standard microsatellite markers (S8); such tumors were excludedbecause of their much higher background mutation rates. All samples wereobtained in accordance with the Health Insurance Portability andAccountability Act (HIPAA).

Laser Capture Microdissection.

20 μm sections of snap frozen primary breast tumor tissues embedded inOCT were deposited on Sigma silane-Prep™ slides and stained withhematoxylin and eosin. Tumor cells were separated from surroundingtissue and recovered on transfer film by laser-capture microdissection(PixCell® lie, Arcturus). Genomic DNA was purified from approximately 20slides for each sample using the Qiagen™ QIAamp® DNA Micro kit accordingto the manufacturer's protocol.

Whole Genome Amplification.

Whole genome amplification was used to provide sufficient quantities ofDNA for the Validation Screen. Briefly, 5-20 ng template DNA wasdenatured with 5 M KOH, neutralized and incubated at 30° C. for 16-24hours with 4×REPLI-g buffer and REPLI-g DNA polymerase according to themanufacturer's instructions (Qiagen, Valencia, Calif.). Samples wereincubated at 65° C. for 3 min to inactivate the enzyme before storage at20° C. For each sample, a minimum of 5 independent WGA reactions werepooled to reduce the effects of any allelic or locus bias that may haveoccurred during amplification.

Confirmation of Sample Identity.

DNA sample identities were monitored throughout the Discovery andValidation Screens by PCR amplification and sequencing of exon 3 of themajor histocompatibility complex gene HLA-A (forward primer5′CGCCTTTACCCGGTTTCATT-3′, SEQ ID NO: 2; reverse primer5′-CCAATTGTCTCCCCTCCTTG-3′, SEQ ID NO: 3). In addition, matching of alltumor-normal pairs was confirmed by typing nine STR loci (TPOX, chr2p23-ter; D3S1358, chr3p; FGA, chr4q28; D8S1179, chr8; TH01, chr11p15.5; vWA, chr12p12-ter; Penta E, chr15q; D18S51, chr18q21.3; 021 S11,chr21 q11-21) using the PowerPlex 2.1 System (Promega, Madison, Wis.).

PCR Amplification and Sequencing.

All primers were synthesized by Invitrogen (San Diego, Calif.). PCR wasperformed in 5 III reactions containing 1×PCR Buffer (67 mM TrisHCl, pH8.8, 6.7 mM MgCb, 16.6 mM NH4S04, 10 mM 2-mercaptoethanol), 1 mM dNTPs(Invitrogen, San Diego, Calif.), 111M forward and 111M reverse primers,6% DMSO, 2 mM ATP, 0.25 U Platinum Taq (Invitrogen, San Diego, Calif.)and 3 ng DNA. Reactions were carried out in 384-well ABI9700thermocyclers (Applied Biosystems, Foster City, Calif.) using atouchdown PCR protocol (1 cycle of 96° C. for 2 min; 3 cycles of 96° C.for 10 see, 64° C. for 10 see, 70° C. for 30 see; 3 cycles of 96° C. for10 see, 61° C. for 10 see, 70° C. for 30 see; 3 cycles of 96° C. for 10see, 58° C. for 10 see, 70° C. for 30 see; 41 cycles of 96° C. for 10see, 57° C. for 10 see, 70° C. for 30 see; 1 cycle of 70° C. for 5 min).Templates were purified using AMPure (Agencourt Biosciences, Beverly,Mass.) and sequencing carried out with M13 forward primer(5′GTAAAACGACGGCCAGT-3; SEQ ID NO: 1) and Big Dye Terminator Kit v. 3.1(Applied Biosystems, Foster City, Calif.). 1% DMSO was included insequencing reactions when the GC content of the template exceeded 65%.Dye terminators were removed using the CleanSEQ kit (AgencourtBiosciences, Beverly, Mass.) and sequence reactions were delineated onABI PRISM 3730×1 sequencing apparatuses (Applied Biosystems, FosterCity, Calif.).

Sequence Assembly and Analysis of Mutations.

Sequence traces from tumor and normal DNA samples were aligned to thegenomic reference sequences. To consider an amplicon successfullysequenced, at least three quarters of the tumors were required to have2′:90% of the bases in the target region with a Phred quality score of20 or better. Amplicons not meeting these criteria were not analyzedfurther. Mutational analysis was performed for all coding exonicsequences and the flanking 4 bp of intronic or UTR sequences usingMutation Surveyor (Softgenetics, State College, Pa.) coupled to arelational database (Microsoft SQL Server). For both Mutation Discoveryand Validation Screens, the following basic steps were employed toidentify mutations of interest. First, synonymous changes wereidentified and excluded from further analysis. Second, nonsynonymouschanges in tumor samples were discarded if an identical change waspresent in a normal DNA sample. Third, known single nucleotidepolymorphisms were removed by comparison to a database of dbSNP entriespreviously validated by the Hap Map project. Finally, false positiveartifacts were eliminated by visual inspection of chromatograms for eachsample with a putative mutation. Additional steps are described below.

Mutation Discovery Screen.

Primers designed above were used to amplify all known CCDS exons from 11colorectal cancer samples, 11 breast cancer samples, and two matchednormal DNA samples. This resulted in a total of −3.25 million PCRreactions, comprising 465 Mb of tumor-derived sequences as well as atotal of 42 Mb of normal sequences from the two matched normal DNAsamples. Following sequence assembly and mutational analysis, eachobserved putative nonsynonymous change was confirmed in an independentPCR reaction using the same primer pair. Upon confirmation, DNA from anormal tissue of the same patient was used to determine whether theobserved mutation was a true somatic event rather than a germ linevariant. When the same putative mutation was observed in multiple tumorsamples, only a single tumor and matched normal sample were initiallyused to confirm the mutation and its somatic mutation. If confirmed, DNAfrom the other tumors containing the same somatic mutation weresimilarly evaluated. To exclude the possibility that putative somaticmutations might be caused by amplification of homologous butnon-identical sequences, BLAT (58) was used to search these sequencesagainst the human genome. This examination ensured that the nucleotidechange was not present in a highly related region in the human genome.For putative somatic mutations found in xenografted tumors, BLAT wasused to similarly search the mouse genome to exclude the contribution ofhomologous mouse sequences.

Mutation Validation Screen.

Every gene found mutated in the Discovery Screen was further analyzed byamplification and sequencing of 24 additional tumor samples of the sametissue type. Because of limiting amounts of sample DNA, the set of 24tumors evaluated changed over time. All CCDS transcript variants of thegene of interest were investigated using primer pairs that yieldedinformative sequences in the Discovery Screen. Mutation detection,confirmation of alterations, and determination of somatic status wasperformed as above, with the exception that all germ line variantspreviously observed in the normal DNA samples of the Discovery Screenwere considered to be known variants (FIG. 1).

Statistical Analyses.

CaMP Scores.

To help identify genes that were mutated more frequently than would beexpected in the absence of selection, we first computed the probabilitythat a given gene was mutated the observed number of times given thebackground mutation frequency. The background mutation frequency inbreast and co lorecta I cancers has been previously determined to beless than 1.2 mutations per Mb (59-511). Comparison of the prevalence ofsynonymous vs. non-synonymous mutations can be useful predictors ofgenes that had undergone selection, as it can be assumed that synonymousmutations are generally nonfunctional (511-515). However, relatively fewmutations were detected in most genes in many of the tumors we studied,leading to wide confidence limits in this parameter. We therefore used acombination of experimental validation and an estimate of the backgroundmutation rate to identify those genes most likely to have undergoneselection.

To correct for the influence of nucleotide composition on the likelihoodof mutation, we assumed that the mutation spectrum observed in thecurrent study was no different from that of unselected backgroundmutations and that both were a result of the same underlying processesand exposures to exogenous agents. The table below shows the backgroundmutation frequency per Mb at each of the six nucleotide contexts andpositions analyzed. For example, in our Discovery and Validation screensin colorectal cancers, we found that mutations at 5′-CpG-3′ mutationswere 6.44 more frequent than the mutation frequency at all positionscombined. The expected background mutation frequency at 5′-CpG-3′ siteswas therefore calculated to be 6.44×1.2=7.73 mutations per million bp.

Estimated Background Mutation Frequencies Per Million Bp.

INS/ DEL/ 5′-CpG-3′ 5′-TpC-3′ A C G T DUP Colorectal 7.73 0.96 0.56 0.950.85 0.51 0.55 Breast 2.99 2.48 0.76 1.38 1.07 0.30 0.55

For each gene and tumor type, the number of successfully sequenced5′-CpG-3′ and 5′-TpC3′ (or complementary 5′-GpA-3′) dinucleotide sitesand A, C, T, and G mononucleotide sites were designated NcpG, NTpC, NA,Nc, NG, and NT, respectively. N_(c) did not include those C's within5′-CpG or 5′-TpC dinucleotides and NG did not include those G's within5′-CpG-3′ or 5′GpA-3 dinucleotides. Note that mutations at 5′-TpC-3′sites were nearly always at the C residue and mutations at thecomplementary 5′-GpA-3′ sites were nearly always at the G residue,explaining why the A's and T's did not need to be corrected for theirpresence within dinucleotides. The probability of a gene having theobserved number of mutations at a particular site was then calculatedwith an exact binomial distribution. For example, the parameters forthis calculation for the 5′-CpG-3′ category used the observed number ofmutations at 5′-CpG-3′ sites as the number of positive events, NcpG asthe number of independent trials, and the background mutationfrequencies for NcpG listed in the table above (7.73×10-6 for colorectalcancers) as the probability of a positive result in each trial. Theprobabilities of a gene having the observed number of mutations at eachof the other five dinucleotide or mononucleotides were similarlycalculated. The probability of a gene containing the observed number ofinsertions, deletions, or duplications (INS/DEL/DUP) was calculated byusing a binomial distribution with the following parameters: observednumber of INS/DEL/DUP events as the number of positive events, totalnucleotides successfully sequenced within the gene as the number ofindependent trials, and 0.55×10⁻⁶ as the probability of a positiveresult in each trial. Note that each of these seven probabilities wasconsidered to be independent. The probability of a gene having theobserved number of mutations at the observed positions was thencalculated to be the product of the seven nucleotide context-specificprobabilities.

As 13,023 genes were evaluated for mutations, it was necessary tocorrect these probabilities for multiple comparisons. For this purpose,we used the algorithm described by Benjamini and Hochberg (S16). Thegenes were ranked in ascending order, assigning a 1 to the gene with thelowest probability of having the observed number of mutations in it, a 2to the gene with the next lowest probability, etc. The CaMP score foreach gene was then defined as −log₁₀(13,023*PROB/RANK), where PROB isthe probability of its having the observed number of mutations and RANKrepresents its numerical position in the list. A Microsoft Excel™spreadsheet that automatically calculates CaMP scores for individual ormultiple genes is available from the authors upon request.

Statistical Significance of Data in FIGS. 5-6 (Tables 1 and 2) and FIG.15 (FIG. S1).

To determine whether the observed number of mutations in the entire setof breast and colorectal cancers differed significantly from theexpected number of mutations (FIG. 5; Table 1), a simple binomialdistribution test was used, employing a probability of 1.2×10⁻⁶ as thebackground rate. The spectrum of mutations was compared in breast andcolorectal cancers (FIG. 6; Table 2) using a Chi-Square test.

The spectrum of codons affected by mutation (FIG. 15; FIG. S1) was alsoanalyzed with a Chi-Square test.

Estimate of Non-Synonymous Mutations in the Cancer Genome.

The total number of genes containing non-synonymous mutations in atypical colorectal or breast cancer was estimated in the following way.Although the actual number of protein coding genes in the human genomeis still a matter of debate, there are 5180 genes for which excellentsupporting evidence exists and which are part of RefSeq (S17) but arenot yet included in the CCOS database. We assumed that the mutationprevalence in genes that have not yet been sequenced is similar to thatof the genes already sequenced. Additionally, we were not able tosuccessfully sequence −10% of the bases within the coding sequences ofthe 13,023 CCOS genes (equivalent to 1,302 unsequenced genes). Wethereby estimate that we have successfully sequenced 64% of the 18,203protein-encoding genes in the human genome (13023−1302)/(13023+5180). Aswe identified an average of 60 mutated genes per tumor in the genesalready sequenced, 93 genes (6010.64) would be predicted to be mutatedin the entire compendium of protein encoding genes in a typical cancer.

REFERENCES

The disclosure of each reference cited is expressly incorporated herein.

-   1. B. Vogelstein, K. W. Kinzler, Nature Med 10, 789 (2004).-   2. P. A. Futreal et al., Nature Rev Cancer 4, 177 (2004).-   3. A. Bardelli, V. E. Velculescu, Curr Opin Genet Dev 15, 5 (2005).-   4. B. Vogelstein, K. W. Kinzler, The Genetic Basis of Human Cancer    (McGraw-Hill, Toronto, 2002)-   5. D. M. Parkin, F. Bray, J. Ferlay, P. Pisani, CA Cancer J Clin 55,    74 (2005).-   6. world wide web domain: ncbi.nlm.nih.gov, database: CCDS.-   7. Materials and methods are available as supporting material at    Science Online.-   8. B. Ewing, P. Green, Genome Res 8, 186 (1998).-   9. C. Lengauer, K. W. Kinzler, B. Vogelstein, Nature 396, 643    (1998).-   10. L. A. Loeb, Cancer Res 61, 3230 (2001).-   11. C. Greenman, R. Wooster, P. A. Futreal, M. R. Stratton, D. F.    Easton, Genetics 173, 2187 (2006).-   12. S. E. Kern, J. M. Winter, Cancer Biol Ther 5, 349 (2006).-   13. T. L. Wang et al., Proc Natl Acad Sci USA 99, 3076 (2002).-   14. D. Shen et al., Submitted (2006).-   15. P. Stephens et al., Nat Genet 37, 590 (2005).-   16. H. Strohmaier et al., Nature 413, 316 (2001).-   17. A. Bardelli et al., Science 300, 949 (2003).-   18. Z. Wang et al., Cancer Res 64, 2998 (2004).-   19. G. J. Riggins, et al. Nat Genet 13, 347 (1996).-   20. K. Eppert et al., Cell 86, 543 (1996).-   21. J. L. Ku et al., Cancer Lett (Jul. 5, 2006).-   22. A. Duval et al., Cancer Res 59, 4213 (1999).-   23. S. Markowitz et al., Science 268, 1336 (1995).-   24. C. A. Landis et al., Nature 340, 692 (1989).-   25. B. Padmanabhan et al., Mol Cell 21, 689 (2006).-   26. O. Bluteau et al., Nat Genet 32, 312 (2002).-   27. K. Salassidis et al., Cancer Res 60, 2786 (2000).-   28. Y. Arai et al., Blood 89, 3936 (1997).-   29. K. W. Kinzler et al., Science 236, 70 (1987).-   30. H. Varmus, Science 312, 1162 (2006).-   31. X. X. Tang, G. M. Brodeur, B. G. Campling, N. Ikegaki, Clin    Cancer Res 5, 455 (1999).-   32. M. Ruault, M. E. Brun, M. Ventura, G. Roizes, A. De Sario, Gene    284, 73 (2002).-   33. M. Tanaka et al., Cancer Res 55, 3228 (1995).-   34. A. Sasaki, Y. Masuda, Y. Ohm, K. Ikeda, K. Watanabe, J Biol Chem    276, 17871 (2001).-   35. M. Sato et al., Genes Chromosomes Cancer 44, 405 (2005).-   36. Y. Onishi, K. Tsukada, J. Yokota, A. Raz, Clin Exp Metastasis    20, 51 (2003).-   37. M. Hollstein, D. Sidransky, B. Vogelstein, C. C. Harris, Science    253, 49 (1991).-   38. J. L. Bos et al., Nature 327, 293 (1987).-   39. R. Brent, Cell 100, 169 (2000).-   40. T. Ideker et al., Science 292, 929 (2001).-   41. S. L. Ooi et al., Trends Genet 22, 56 (2006).-   42. T. Soussi, G. Lozano, Biochem Biophys Res Commun 331, 834    (2005).-   43. M. Olivier, S. P. Hussain, C. Caron de Fromentel, P.    Hainaut, C. C. Harris, IARC Sci Publ, 247 (2004).-   44. J. F. Costello et al., Nat Genet 24, 132 (2000).-   45. A. H. Owens, Coffey, D. S., and Baylin, S. B., eds., Tumor Cell    Heterogeneity. (Academic Press, New York, 1982), pp. pp. 441-460.-   46. K. D. Pruitt, T. Tatusova, D. R. Maglott, Nucleic Acids Res 33,    D501 (2005).-   47. world wide web domain: cancergenome.nih.gov; document:    index.asp Y. H. Rogers, J. C. Venter. Nature 437, 326 (2005).

1. A method of treating a breast cancer in a human, comprising the stepsof: determining in a test sample relative to a normal sample of thehuman, a somatic mutation in a gene or its encoded cDNA or protein, saidgene selected from the group consisting of those listed in FIG. 13(Table S5); identifying the sample as breast cancer when the somaticmutation is determined; and administering a medical intervention to thehuman when the human is identified as having the somatic mutation in thetest sample.
 2. The method of claim 1 wherein the mutation is selectedfrom those shown in FIG. 12 (Table S4).
 3. The method of claim 1 whereinthe gene is selected from the group consisting of: gelsolin GSN,cadherin genes CDH10 and CDH20, actin and SMAD binding protein filamin BFLNB, and autocrine motility factor receptor AMFR.
 4. The method ofclaim 1 wherein the gene is selected from the group consisting of:ATP-dependent transporter ATP8B1, intrinsic factor-cobalamin receptorCUBN, actin binding protein DBN1, and tectorin alpha TECTA.
 5. Themethod of claim 1 wherein the test sample is a breast tissue sample or asuspected breast cancer metastasis.
 6. The method of claim 1 wherein thenormal sample is a breast tissue sample. 7-12. (canceled)
 13. A methodfor testing a candidate or known anti-cancer therapeutic, comprising thesteps of: determining a CAN-gene mutational signature for a breastcancer by determining at least one somatic mutation in a test samplerelative to a normal sample of a human, wherein the at least one somaticmutation is in one or more genes selected from the group consisting ofFIG. 13 (Table S5); forming a first group of breast cancers that havethe CAN-gene mutational signature; comparing efficacy of the candidateor known anti-cancer therapeutic on the first group to efficacy on asecond group of breast cancers that has a different CAN-gene mutationalsignature; identifying a CAN gene mutational signature which correlateswith increased or decreased efficacy of the candidate or knownanti-cancer therapeutic relative to other groups.
 14. The method ofclaim 13 wherein the at least one mutation is selected from those shownin FIG. 12 (Table S4).
 15. The method of claim 13 wherein the at leastone mutation is in one or more genes selected from the group consistingof: gelsolin GSN, cadherin genes CDH10 and CDH20, actin and SMAD bindingprotein filamin B FLNB, and autocrine motility factor receptor AMFR. 16.The method of claim 13 wherein the at least one mutation is in one ormore genes selected from the group consisting of: ATP-dependenttransporter ATP8B1, intrinsic factor-cobalamin receptor CUBN, actinbinding protein DBN1, and tectorin alpha TECTA.
 17. The method of claim13 wherein the test sample is a breast tissue sample.
 18. The method ofclaim 13 wherein the normal sample is a breast tissue sample.
 19. Themethod of claim 13 wherein the CAN-gene mutational signature comprisesat least 2 genes selected from FIG. 13 (Table S5)
 20. The method ofclaim 13 wherein the CAN-gene mutational signature comprises at least 3genes selected from FIG. 13 (Table S5).
 21. The method of claim 13wherein the CAN-gene mutational signature comprises at least 4 genesselected from FIG. 13 (Table S5).
 22. The method of claim 13 wherein theCAN-gene mutational signature comprises at least 5 genes selected fromFIG. 13 (Table S5).
 23. The method of claim 13 wherein the CAN-genemutational signature comprises at least 6 genes selected from FIG. 13(Table S5).
 24. The method of claim 13 wherein the CAN-gene mutationalsignature comprises at least 7 genes selected from FIG. 13 (Table S5).25-48. (canceled)